Last updated: 2018-09-17

workflowr checks: (Click a bullet for more information)

✔ R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
✔ Seed: set.seed(20180723)

The command set.seed(20180723) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

✔ Repository version: 4797e87

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/.Rhistory
    Ignored:    data/.DS_Store
    Ignored:    docs/.DS_Store
    Ignored:    docs/figure/.DS_Store

Untracked files:
    Untracked:  analysis/drugheatmap.pdf
    Untracked:  analysis/drugheatmap_color_2.pdf
    Untracked:  analysis/drugheatmap_goslim.pdf
    Untracked:  analysis/drugheatmap_target_color.pdf
    Untracked:  analysis/drugheatmap_target_nodup.pdf
    Untracked:  analysis/druginfo.total.csv
    Untracked:  analysis/druginfo_total.csv
    Untracked:  analysis/fifthheatmap.pdf
    Untracked:  analysis/firstheatmap.pdf
    Untracked:  analysis/fourthheatmap.pdf
    Untracked:  analysis/gdsc.Rmd
    Untracked:  analysis/gdsc_drugheatmap_target.pdf
    Untracked:  analysis/gdsccorr.Rmd
    Untracked:  analysis/gene_set_example.Rmd
    Untracked:  analysis/heatmap.pdf
    Untracked:  analysis/regsva_z_row.Rdata
    Untracked:  analysis/secondheatmap.pdf
    Untracked:  analysis/test.tsv
    Untracked:  analysis/thirdheatmap.pdf
    Untracked:  data/CCLE/
    Untracked:  data/GDSC/
    Untracked:  data/GSE36133_series_matrix.txt
    Untracked:  data/Gene_regulators/
    Untracked:  data/gogsva_z_col.Rdata
    Untracked:  data/regsva_new_z_col.Rdata
    Untracked:  data/regsva_z_col.Rdata
    Untracked:  data/regsva_z_row.Rdata
    Untracked:  data/regsva_zscore.Rdata
    Untracked:  docs/drugheatmap.pdf
    Untracked:  docs/figure/correlation analysis.Rmd/
    Untracked:  docs/figure/drug.Rmd/
    Untracked:  docs/figure/gene_set_analysis_re.Rmd/
    Untracked:  docs/goslim_cor_lab_heatmap(reorder).pdf
    Untracked:  docs/goslim_cor_lab_heatmap.pdf

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/correlation_analysis.Rmd
    Modified:   analysis/drugresponse.Rmd
    Modified:   analysis/gene_set_analysis.Rmd
    Modified:   data/README.md

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	4797e87	bingrus	2018-09-17	wflow_publish(“analysis/drugcorr.Rmd”)
html	43550df	bingrus	2018-09-17	Build site.
Rmd	2491680	bingrus	2018-09-17	wflow_publish(“analysis/drugcorr.Rmd”)
html	f336803	bingrus	2018-09-10	Build site.
Rmd	07e682c	bingrus	2018-09-10	wflow_publish(“analysis/drugcorr.Rmd”)
html	53fa8df	bingrus	2018-09-10	Build site.
Rmd	3e40637	bingrus	2018-09-10	wflow_publish(“analysis/drugcorr.Rmd”)
html	7fadc67	bingrus	2018-09-10	Build site.
html	8b2a59e	bingrus	2018-09-10	Build site.
html	5327d89	bingrus	2018-09-10	Build site.
Rmd	37313f4	bingrus	2018-09-10	wflow_git_commit(“analysis/drugcorr.Rmd”)

drug correlation analysis with target sets

method

scale the microarrary expression data for each sample to z-score accross all genes
do ssgsea on the converted microarray expression data
compute correlation scores for ssgsea score to the drug response data (IC50)

Result 1: drug correlation analysis with targets sets

pdf figure with dendogram

interactive figure without dendogram (same order)

interactive figure with target set class labels

interactive figure with regulator age labels

Result 2: the information on the cluster drugs

	Target.s.	Mechanism.of.action	Class	group
17-AAG	HSP90	Heat Shock Protein 90 (hsp90) Inhibitor	Other targeted therapies	1
AZD6244	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	1
PD-0325901	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	1
AEW541	IGF-1R	IGF-1R Inhibitor	Kinase inhibitor	2
Irinotecan	Topoisomerase I	NA	NA	2
L-685458	Gamma Secretase	gamma-Secretase Inhibitor	Other targeted therapies	2
Nutlin-3	MDM2	MDM2 Inhibitor	Other targeted therapies	2
Paclitaxel	beta-tubulin	Microtubule-Stabilizing Agents	Cytotoxic	2
Panobinostat	HDAC	Histone Deacetylase (HDAC) Inhibitor	Other targeted therapies	2
PF2341066	c-MET, ALK	c-MET and ALK Inhibitor	Kinase inhibitor	2
RAF265	Raf kinase B, KDR	Raf kinase B and KDR Inhibitor	Kinase inhibitor	2
Sorafenib	Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	2
TAE684	ALK	ALK Inhibitor	Kinase inhibitor	2
TKI258	EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR	Multi-kinase inhibitor	Kinase inhibitor	2
Topotecan	Topoisomerase I	DNA Topoisomerase I Inhibitor	Cytotoxic	2
AZD0530	Src, Abl/Bcr-Abl, EGFR	Src and Abl inhibitor	Kinase inhibitor	3
Erlotinib	EGFR	EGFR Inhibitor	Kinase inhibitor	3
Lapatinib	EGFR, HER2	EGFR and HER2 Inhibitor	Kinase inhibitor	3
ZD-6474	Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	3
LBW242	IAP	Inhibitor of Apoptosis Proteins (IAP) Inhibitor	Other targeted therapies	4
Nilotinib	Abl/Bcr-Abl	Abl Inhibitor	Kinase inhibitor	4
PD-0332991	CDK4/6	CDK4/6 Inhibitor	Kinase inhibitor	4
PHA-665752	c-MET	c-MET Inhibitor	Kinase inhibitor	4
PLX4720	RAF	Raf kinase B Inhibitor	Kinase inhibitor	5

Result 3: drug response correlate with goslim

Expand here to see past versions of drugheatmap_goslim.pdf:

Version	Author	Date
c1d5012	bingrus	2018-09-10

interactive plot

	Target.s.	Mechanism.of.action	Class	group
17-AAG	HSP90	Heat Shock Protein 90 (hsp90) Inhibitor	Other targeted therapies	1
AZD0530	Src, Abl/Bcr-Abl, EGFR	Src and Abl inhibitor	Kinase inhibitor	1
AZD6244	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	1
Erlotinib	EGFR	EGFR Inhibitor	Kinase inhibitor	1
Lapatinib	EGFR, HER2	EGFR and HER2 Inhibitor	Kinase inhibitor	1
PD-0325901	MEK	MEK1 and MEK2 Inhibitor	Kinase inhibitor	1
ZD-6474	Abl, EGFR, Flt3, C-KIT, RET, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	1
AEW541	IGF-1R	IGF-1R Inhibitor	Kinase inhibitor	2
Nilotinib	Abl/Bcr-Abl	Abl Inhibitor	Kinase inhibitor	2
PD-0332991	CDK4/6	CDK4/6 Inhibitor	Kinase inhibitor	2
PHA-665752	c-MET	c-MET Inhibitor	Kinase inhibitor	2
RAF265	Raf kinase B, KDR	Raf kinase B and KDR Inhibitor	Kinase inhibitor	2
Irinotecan	Topoisomerase I	NA	NA	3
Topotecan	Topoisomerase I	DNA Topoisomerase I Inhibitor	Cytotoxic	3
L-685458	Gamma Secretase	gamma-Secretase Inhibitor	Other targeted therapies	4
Nutlin-3	MDM2	MDM2 Inhibitor	Other targeted therapies	4
Paclitaxel	beta-tubulin	Microtubule-Stabilizing Agents	Cytotoxic	4
Panobinostat	HDAC	Histone Deacetylase (HDAC) Inhibitor	Other targeted therapies	4
PF2341066	c-MET, ALK	c-MET and ALK Inhibitor	Kinase inhibitor	4
Sorafenib	Flt3, C-KIT, PDGFRbeta, RET, Raf kinase B, Raf kinase C, VEGFR-1, KDR, FLT4	Multi-kinase inhibitor	Kinase inhibitor	4
TAE684	ALK	ALK Inhibitor	Kinase inhibitor	4
TKI258	EGFR, FGFR1, PDGFRbeta, VEGFR-1, KDR	Multi-kinase inhibitor	Kinase inhibitor	4
LBW242	IAP	Inhibitor of Apoptosis Proteins (IAP) Inhibitor	Other targeted therapies	5
PLX4720	RAF	Raf kinase B Inhibitor	Kinase inhibitor	5

Session information

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] org.Hs.eg.db_3.6.0   kableExtra_0.9.0     knitr_1.20          
 [4] GSEABase_1.42.0      graph_1.58.0         annotate_1.58.0     
 [7] XML_3.98-1.16        AnnotationDbi_1.42.1 IRanges_2.14.11     
[10] S4Vectors_0.18.3     GSVA_1.28.0          heatmaply_0.15.2    
[13] viridis_0.5.1        viridisLite_0.3.0    plotly_4.8.0        
[16] ggplot2_3.0.0        dplyr_0.7.6          gplots_3.0.1        
[19] GEOquery_2.48.0      Biobase_2.40.0       BiocGenerics_0.26.0 
[22] reshape_0.8.7       

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2    class_7.3-14        modeltools_0.2-22  
  [4] mclust_5.4.1        rprojroot_1.3-2     rstudioapi_0.7     
  [7] flexmix_2.3-14      bit64_0.9-7         mvtnorm_1.0-8      
 [10] xml2_1.2.0          codetools_0.2-15    R.methodsS3_1.7.1  
 [13] robustbase_0.93-2   geneplotter_1.58.0  shinythemes_1.1.1  
 [16] jsonlite_1.5        workflowr_1.1.1     cluster_2.0.7-1    
 [19] kernlab_0.9-27      R.oo_1.22.0         shiny_1.1.0        
 [22] readr_1.1.1         compiler_3.5.0      httr_1.3.1         
 [25] backports_1.1.2     assertthat_0.2.0    lazyeval_0.2.1     
 [28] limma_3.36.3        later_0.7.3         htmltools_0.3.6    
 [31] tools_3.5.0         bindrcpp_0.2.2      gtable_0.2.0       
 [34] glue_1.3.0          reshape2_1.4.3      Rcpp_0.12.18       
 [37] trimcluster_0.1-2.1 gdata_2.18.0        crosstalk_1.0.0    
 [40] iterators_1.0.10    fpc_2.1-11.1        stringr_1.3.1      
 [43] rvest_0.3.2         mime_0.5            gtools_3.8.1       
 [46] dendextend_1.8.0    DEoptimR_1.0-8      MASS_7.3-50        
 [49] scales_1.0.0        TSP_1.1-6           hms_0.4.2          
 [52] promises_1.0.1      RColorBrewer_1.1-2  yaml_2.2.0         
 [55] memoise_1.1.0       gridExtra_2.3       stringi_1.2.4      
 [58] RSQLite_2.1.1       highr_0.7           gclus_1.3.1        
 [61] foreach_1.4.4       seriation_1.2-3     caTools_1.17.1.1   
 [64] rlang_0.2.2         pkgconfig_2.0.2     prabclus_2.2-6     
 [67] bitops_1.0-6        evaluate_0.11       lattice_0.20-35    
 [70] purrr_0.2.5         bindr_0.1.1         labeling_0.3       
 [73] htmlwidgets_1.2     bit_1.1-14          tidyselect_0.2.4   
 [76] plyr_1.8.4          magrittr_1.5        R6_2.2.2           
 [79] DBI_1.0.0           pillar_1.3.0        whisker_0.3-2      
 [82] withr_2.1.2         RCurl_1.95-4.11     nnet_7.3-12        
 [85] tibble_1.4.2        crayon_1.3.4        KernSmooth_2.23-15 
 [88] rmarkdown_1.10      grid_3.5.0          data.table_1.11.4  
 [91] blob_1.1.1          git2r_0.23.0        digest_0.6.16      
 [94] diptest_0.75-7      webshot_0.5.0       xtable_1.8-3       
 [97] tidyr_0.8.1         httpuv_1.4.5        R.utils_2.7.0      
[100] munsell_0.5.0       registry_0.5

This reproducible R Markdown analysis was created with workflowr 1.1.1

Drug correlation